Fix invalid file bug with iter_files (#764)

# Motivation

<!-- Why is this change necessary? -->

# Content

<!-- Please include a summary of the change -->

# Testing

<!-- How was the change tested? -->

# Please check the following before marking your PR as ready for review

- [ ] I have added tests for my changes
- [ ] I have updated the documentation or added new documentation as
needed

Author: EdwardJXLi

src/codegen/extensions/tools/semantic_edit.py

@@ -109,7 +109,7 @@ def get_llm_edit(original_file_section: str, edit_content: str) -> str:
 
 
 def _validate_edit_boundaries(original_lines: list[str], modified_lines: list[str], start_idx: int, end_idx: int) -> None:
-    """Validate that the edit only modified lines within the specified boundaries.
+    """Validate` that the edit only modified lines within the specified boundaries.
 
     Args:
         original_lines: Original file lines

src/codegen/git/repo_operator/repo_operator.py

@@ -643,13 +643,14 @@ def iter_files(
 
             if extensions is None or any(filepath.endswith(e) for e in extensions):
                 try:
-                    if not skip_content:
-                        content = self.get_file(filepath)
-                        yield rel_filepath, content
+                    if os.path.isfile(filepath):
+                        if not skip_content:
+                            content = self.get_file(filepath)
+                            yield rel_filepath, content
+                        else:
+                            yield rel_filepath, ""
                     else:
-                        # WTF??? A no-op file read here fixes file parsing somehow?
-                        open(filepath).close()
-                        yield rel_filepath, ""
+                        logger.warning(f"Skipping {filepath} because it does not exist or is not a valid file.")
                 except Exception as e:
                     logger.warning(f"Error reading file {filepath}: {e}")